Likelihood-based Assignment Research Articles

Methodological Bias in Estimates of Strain Composition and Straying of Hatchery-Produced Steelhead in Lake Michigan Tributaries

Steelhead Oncorhynchus mykiss were first introduced into the Great Lakes in the late 1800s. Subsequently, natural recruitment of steelhead from spawning runs in streams across the basin has been regularly supplemented by hatchery production of strains derived from widely dispersed locales within the species' native range. Estimates of hatchery contributions to the spawning runs of naturalized populations may be underrepresented by observations of marked fish, as not all hatchery fish are marked prior to release. To assess the potential bias in estimates of the hatchery contribution to steelhead spawning runs in four major rivers in Michigan, we used scale pattern analysis (SPA) to identify nonmarked hatchery fish and multilocus genotypes to estimate the proportional contributions of each hatchery strain to spawning runs. The four hatchery strains currently stocked are significantly genetically distinct (mean FST = 0.077), making it possible to identify specific strains by use of likelihood-based assignment tests. The differences between direct (mark observations) and indirect (SPA and genetic analysis) estimates of hatchery contribution were mainly due to variations in the percentage of hatchery fish marked by states prior to release and the potential for confusion between certain marks and injuries. By combining direct and indirect assessment methodologies, we estimated that the percentage of hatchery fish returning to the four rivers ranged from 13% to 31% of total spawning runs. The large contribution of hatchery fish to nonstocked rivers differed significantly from expectations of strain-specific stocking rates across the Lake Michigan basin and for individual streams, indicating high amounts of straying into Michigan streams.

IDENTIFICATION OF SOURCE POPULATION FOR GREENLAND CANADA GEESE: GENETIC ASSESSMENT OF A RECENT COLONIZATION

Abstract We used microsatellite markers, mitochondrial DNA (mtDNA), and satellite telemetry to infer the North American geographic origin and racial composition of Canada Geese (Branta canadensis) from newly colonized habitats in Greenland. Using likelihood-based assignment tests we determined that multilocus genotypes of Greenland Canada Geese were consistent with the hypothesis of origin from birds of the Atlantic Population breeding around southern Ungava Bay, Quebec, Canada. The Atlantic Population, based on previous studies of seasonal movements and demography, appeared to be reproductively isolated from the North Atlantic Population. We found that these two populations were genetically differentiated based on microsatellite allele and mtDNA haplotype frequencies. Findings of high levels of genetic discordance among North American breeding populations are consistent with migratory movements, despite high levels of distributional overlap of birds from the North Atlantic and Atlantic Populations during...

Microsatellite analysis of multiple paternity and male reproductive success in the promiscuous snowshoe hare

Few genetic studies have addressed patterns of paternity in promiscuous mammals. I used microsatellite DNA primers developed in the European rabbit to analyze paternity in the promiscuous snowshoe hare (Lepus americanus). Sixty-five offspring, their 12 mothers, and their 24 putative fathers were genotyped at seven polymorphic loci (3–22 alleles/locus). Paternal allele counts and likelihood-based paternity assignments confirmed that multiple paternity occurs in snowshoe hare litters. However, the estimated frequency of multiple paternity was lower than expected in an unstructured promiscuous mating system. A relatively low variance in male reproductive success indicated that no males dominated paternity. A few males did achieve significantly more paternities than average, largely by fathering one or two complete litters rather than a few offspring in many litters. The results suggest that successful multiple mating is limited among both male and female snowshoe hares. An important role for pre- and (or) post-copulatory competition is implied.

Assignment of Individuals to Populations: Bayesian Methods and Multi-Locus Genotypes

Multi-locus genotype data have become a powerful management tool to identify degree of population structure, assign individuals to populations, identify hybridization, and assess rates of migration between populations. We use an example from the tuberculosis (TB)-infected white-tailed deer (Odocoileus virginianus) population in northeast Michigan (Deer Management Unit [DMU] 452) to illustrate the utility of multi-locus genotype data combined with assignment testing approaches in a wildlife management setting. We used microsatellite loci to establish that an unknown TB-positive deer tissue sample originated from a deer outside DMU452. Subsequently, we used multi-locus genotypic data and a likelihood-based assignment test to place TB-positive deer harvested outside of DMU452 into their populations of origin. We used genetic algorithms to identify a maximally informative subset of loci. We also determined estimates of statistical confidence in individual assignment decisions. Data indicate that the unknown TB-positive deer tissue sample was from a deer harvested outside DMU452. Two TB-positive deer killed outside of DMU452 were assigned to the local populations where they were harvested. The presence of TB-positive deer outside DMU452 suggests that TB is present in multiple areas of Michigan, dictating increased surveillance and changes in management policy for white-tailed deer throughout the state.